Bioinformatics for LC-MS/MS-Based Proteomics - LC-MS/MS in Proteomics: Methods and Applications - page 72

Reporter ion-based quantitation methods use the relative
intensities of specific fragment peaks at fixed m / z values gener-
ated from chemically derivatized peptides that break down under
MS/MS conditions ( 38 , 39 ) . Precursor quantitation uses the rel-
ative intensities of extracted ion chromatograms (XICs) for pre-
cursors within a single data set. Any chemical derivatization that
creates a large enough precursor mass shift can be used. The
more popular techniques include ICAT ( 40 ) , 18 O labeling ( 41 ,
42 ) , spiking in an isotopically enriched peptide ( 43 ) , and grow-
ing under isotopically enriched conditions ( 44 ) amongst other
methods. For multiplex quantitation, the two samples are differ-
entially labeled at a terminal creating a small mass shift and both
peptides are passed through the MS/MS transmission window for
fragmentation. The relative intensities of sequence ion fragment
peaks are used for the quantitation ( 45 ) . A protocol that is receiv-
ing a lot of attention is the replicate protocol because it is label
free ( 46 - 51 ) . The quantitation is based on the relative intensities
of XICs for the precursors in multiple data sets. Spectral count-
ing is another label-free quantitation protocol and is based on the
number of spectra observed per protein. A variation is the emPAI
method that compares the number of observed spectra against
the number of expected peptides ( 52 ) . The average quantitation
protocol is also a label-free method for quantifying proteins in a
mixture based on the identified peptide's XIC intensities ( 53 ) .
There are quite a few software packages available for quanti-
tation ( Table 4.5 ) . Many of them are restricted to data from a
particular instrument so that they can generate XICs, and this is

Table 4.5
Quantitation software

MSQuant ( 103 ) http://msquant.sourceforge.net/

MaxQuant
( 104 , 105 )

http://www.biochem.mpg.de/en/rd/maxquant/
index.html

Mascot
Distiller

http://www.matrixscience.com/distiller.html

Trans-Proteomic
Pipeline ( 77 )

http://tools.proteomecenter.org/wiki/index.php?
title

= Software:TPP

iTracker ( 106 ) http://www.cranfield.ac.uk/health/researchareas/

bioinformatics/page6801.jsp

MFPaQ ( 107 ) http://mfpaq.sourceforge.net/

DAnTE ( 108 ) http://omics.pnl.gov/software/DAnTE.php

RAAMS ( 109 ) http://informatics.mayo.edu/svn/trunk/mprc/

raams/index.html

StatQuant ( 110 ) https://gforge.nbic.nl/projects/statquant/

ZoomQuant ( 41 ) http://proteomics.mcw.edu/zoomquant